if you are in the ship you want to use the weapons (turrets) simply go to the COMMAND CONSOLE (SHIFT+C) of the ship and from there select the TURRET OPTIONS and set them to ATACK ALL ENEMYES or select one with a fast shooting weapon for MISSILE DEFFENCE.

and thats only the way to let the turrets be controlled by the AIif you want to shoot yourself press F1(button for cycling all camera modes) until you are in the turret you want to be innow you can control it with your mousethis works even if you gave the turret an AI command earlierafter you go out of this turret it will continue the AI command you gave it

and as you mention mods: i can really recommend cmod3 (Combat mod)it rebalances every weapon really good including the damage and speed of the projectiles (and adds better and unique sound- and graphiceffects for every single weapon)

I remember when i played X3:Reunion a while ago, the turrets on the big M1 and M2 ships rearly hit when you are in the system watching/flying one of them. this is because the AI uses visual targeting or something. when you're not in the system, the game uses math to render the outcome of any combats with your AI ships. this works well if you have alot of big ships and want to conquer a sector. just beam in the ships to the sector and just watch them through the map instead.